Weapons arts can seem very distantly, or abstractly, related to Aikido, particularly for the period when you are learning the movements and burning them in. Sometimes it is just impossible to relate the two, way more effort than it is worth. If I ever took up Shindo Muso ryu, for example, I would have to put down the Aikijo for good, because the two systems seem so different to me that it is ridiculous.
To me, too. There just seem to be some different basic assumptions going on. I'm keeping an open mind (going on seven years now) towards aikijo, but so far it just hasn't caught fire in my heart. I wish I still had the opportunity to study Shindo Muso, but I think you're right -- if I did, the Aikijo would just seem wrong, wrong, wrong.